With fast-cgi, custom php.ini needs to be in the cgi-bin folder.

1) Move php.ini to cgi-bin folder

2) In cgi-bin folder, create php.fcgi and put the following in this file:

exec /usr/local/cpanel/cgi-sys/php5

3) chmod php.fcgi to 755.

4) Upload .htaccess under public_html, put the following:

AddHandler php5-fastcgi .php
 Action php5-fastcgi /cgi-bin/php.fcgi


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